Tennessee's COVID-19 variant testing lags as omicron cases grow

Staff file photo / Dawn Richards works at the Baylor Esoteric and Molecular Laboratory in the Weeks Science Building on the campus of Baylor School on Friday, July 17, 2020, in Chattanooga.

Tennessee's ability to detect the presence of coronavirus variants remains extremely limited as the new variant omicron draws worldwide attention, leaving public health officials largely in the dark in terms of knowing if omicron is in the state.

As of Saturday morning, at least 13 states - including neighboring Georgia - had detected at least one omicron case since it was first reported in the United States on Wednesday, according to the U.S. Centers for Disease Control and Prevention. However, it's likely the variant has spread elsewhere given that testing for variants is sporadic and takes more time and resources than routine COVID-19 diagnostics.

Laboratory workers must conduct a technique called genetic sequencing in order to confirm a viral variant. In February, 0.02% of Tennessee's cumulative positive COVID-19 samples - 153 cases - had been sequenced for variants, according to data from the CDC website.

Though Tennessee has since scaled up its variant surveillance, it still lags far behind other states in sequencing despite knowing that new, more dangerous variants are expected to emerge.

The CDC recommends sequencing 5% of all positive COVID-19 samples. As of Nov. 30, Tennessee had sequenced 1.95% of its samples, according to the CDC - placing it among the states conducting the lowest rate of sequencing.

Surveillance for viral variants is necessary to answer important questions, including whether current COVID-19 tests or treatments are still viable or if vaccines need to be tweaked.

Omicron was named a "variant of concern" by the World Health Organization on Nov. 26 due to its significant number of mutations on the virus's signature "spike protein" and the rapid rise in COVID-19 cases in South Africa, where the variant was first identified.

California, which is where the first U.S. omicron case was detected, has sequenced 5.7% of its COVID-19 samples, while Vermont leads the nation with 22.3% of cases sequenced, according to the CDC.

SARS-CoV-2, the virus that causes the disease COVID-19, is constantly evolving through mutations in its genetic code, therefore new variants are expected to emerge. While most mutations are insignificant, occasionally some may give the virus an advantage over previous strains, causing it to replicate and replace previous variants.

"Advantages" could include that the strain is more contagious, causes more severe illness or is better able to evade immunity from vaccinations or prior infections.

(READ MORE: As omicron looms, US is still battling the delta wave)

The delta variant is far and away the dominant coronavirus strain in the United States at this time, but a continued rise in new omicron cases would signal its mutations may allow it to overtake delta. It will take several more weeks for scientists to assess whether omicron is actually more dangerous.

Elizabeth Forrester, founder and technical director at Athena Esoterix - the only lab in the Chattanooga region conducting sequencing for coronavirus variants - said the lab has yet to detect omicron locally, but it's also not doing nearly as much sequencing as it could.

The lab currently foots the bill for all coronavirus sequencing, so it only sequences samples that appear especially concerning, such as a large cluster of cases among vaccinated individuals at a nursing home. Athena Esoterix is capable of conducting more sequencing, but it would need more political will behind the effort, she said.

"If the community wants it, then we have to figure out how to fund it, and we have to make it a priority locally, because we're not going to get the information otherwise," Forrester said, adding that the county hasn't sought available federal funds that would allow them to expand coronavirus sequencing in the Chattanooga region.

A Wednesday statement from the CDC said, "The recent emergence of the omicron variant (B.1.1.529) further emphasizes the importance of vaccination, boosters and general prevention strategies needed to protect against COVID-19. Everyone 5 and older should get vaccinated, and boosters are recommended for everyone 18 years and older."

Contact Elizabeth Fite at efite@timesfreepress.com or follow her on Twitter @ecfite.